Hi, Steve. It's a high resolution epi sequence (1.8 x 1.8 x 3 mm).
This is actually just the pilot test -- the real experiment will have
even more volumes (close to 400; it's currently 300). Would it be
appropriate to cut the file into 2 pieces, run feat on each chunk, and
then run a fixed effects 2nd level analyses across the two (or
three...)? What's the single-process job limit? Is that a parameter
that I can somehow increase? I'm running fsl on a windows 200pro with
3.2 gHz processor.


On 12/13/05, Stephen Smith <[log in to unmask]> wrote:
> Hi - this is a large 4D input file - I guess the resolution is pretty
> high... you are either running out of RAM/SWAP, or going over the
> single-process job size limit for your platform. You should first check
> that you have enough swap. Have you upsampled your data?
>
> Cheers, Steve.
>
>
>
> On Tue, 13 Dec 2005, Mike Cohen wrote:
>
> > Hi, FSLers. I have a very simple Feat job, but it keeps crashing and
> > I'm not sure why. There are 300 epi images (concatenated into a nii.gz
> > file that is 114mb) and one covariate that is entered as a custom one
> > entry per volume, not convolved. What's clear from the report.log
> > (pasted below) is that it can't find the sigmasquareds file, and this
> > file seems not to be created. I've tried rerunning with and without
> > prestats steps and registration, and always the same error. Any ideas?
> > Thanks in advance..
> >
> >
> >
> > Started FEAT at Tue Dec 13 13:06:59     2005 on cohen
> > FEAT output is d:/mikeData/testing/mike_dec13/normal/left2.feat
> >
> > /bin/cp /tmp/feat_LdSJ2c.fsf design.fsf
> >
> > /usr/local/fsl/bin/feat_model design
> > Total original volumes = 300
> >
> > /usr/local/fsl/bin/avwroi
> > d:/mikeData/restingNuac/testing/mike_dec13/normal/rest example_func
> > 150 1
> >
> > /usr/local/fsl/bin/ip
> > d:/mikeData/restingNuac/testing/mike_dec13/normal/rest
> > filtered_func_data 10 -s 2.54777070064 -m mask -I 10000 -t 20.0 -1 |
> > grep THRESHOLD | awk '{ print  }' -
> > 1000
> >
> > rm -rf prefiltered_func_data*
> >
> > /usr/local/fsl/bin/film_gls -rn stats -sa -ms 5 -sp
> > /usr/local/fsl/bin/susan_smooth filtered_func_data design.mat
> > 1000.000000
> > Log directory is: stats
> > Calculating residuals...
> > Completed
> > Estimating residual autocorrelation...
> > Calculating raw AutoCorrs... Completed
> > mode = 2488.68
> > sig = 8799
> > Spatially smoothing auto corr estimates
> > /usr/local/fsl/bin/susan_smooth stats/preSmoothVol 1
> > stats/postSmoothVol 5 3D 0 1 stats/epivolume 2933 stats/usanSize
> > ................
> > rm -rf stats/postSmoothVol* stats/preSmoothVol* stats/usanSize*
> > Completed
> > Tukey M = 17
> > Tukey estimates... Completed
> > Completed
> > Prewhitening and Computing PEs...
> > Percentage done:
> > 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,
> > 29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,
> > 54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,
> > 79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,Completed
> > Saving results...
> >
> > /usr/local/fsl/bin/contrast_mgr  stats design.con
> > ** ERROR: nifti_image_read(stats/sigmasquareds): can't open header file
> > ** ERROR: nifti_image_open(stats/sigmasquareds): bad header info
> > Error: failed to open file stats/sigmasquareds
> > Error:: FslGetDim: Null pointer passed for FSLIO
> > Rendering using zmin=2.3 zmax=8
> >
> > mkdir tsplot
> >
> > /usr/local/fsl/bin/tsplot . -f filtered_func_data -o tsplot
> > ** ERROR: nifti_image_read(./stats/pe1): can't open header file
> > ** ERROR: nifti_image_open(./stats/pe1): bad header info
> > Error: failed to open file ./stats/pe1
> > ERROR: Could not open image ./stats/pe1
> > Image Exception : #22 :: Failed to read volume ./stats/pe1
> >
> > /bin/mkdir reg
> >
> > /usr/local/fsl/bin/flirt -ref highres -in example_func -out
> > example_func2highres -omat example_func2highres.mat -cost corratio
> > -dof 6 -schedule /usr/local/fsl/etc/flirtsch/sch3Dtrans_3dof -searchrx
> > -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear
> >
> > /usr/local/fsl/bin/convert_xfm -matonly -inverse -omat
> > highres2example_func.mat example_func2highres.mat
> >
> > /usr/local/fsl/bin/slicer example_func2highres highres -s 1 -x 0.35
> > sla -x 0.45 slb -x 0.55 slc -x 0.65 sld -y 0.35 sle -y 0.45 slf -y
> > 0.55 slg -y 0.65 slh -z 0.35 sli -z 0.45 slj -z 0.55 slk -z 0.65 sll ;
> > /usr/local/fsl/bin/convert -colors 100 +append sla slb slc sld sle slf
> > slg slh sli slj slk sll example_func2highres.gif ; /bin/rm -f sla slb
> > slc sld sle slf slg slh sli slj slk sll
> > Finished registration at Tue Dec 13 13:35:57     2005
> >
> > Finished FEAT at Tue Dec 13 13:35:57     2005
> > To view the FEAT report point your web browser at
> > d:/mikeData/testing/mike_dec13/normal/left2.feat/report.html
> >
>
> --
>  Stephen M. Smith  DPhil
>  Associate Director, FMRIB and Analysis Research Coordinator
>
>  Oxford University Centre for Functional MRI of the Brain
>  John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
>  +44 (0) 1865 222726  (fax 222717)
>
>  [log in to unmask]  http://www.fmrib.ox.ac.uk/~steve
>


--
Mike Cohen
UC Davis Psychology
Epilepsy and Psychiatry Clinics, Bonn, Germany
http://www.DynamicMemoryLab.org/mcohen